PCA and DE analysis for proteins

Chrunks

• Load libraries
• Read in tables
• Proteomic data preparation
  • QC.1 - Intensity and normalized intensity
    • Data preparation
    • Box plot
    • Scatter plot
  • QC.2 - Ratio and normalized ratio
    • Data preparation
    • Box plot
    • Scatter plot
  • Combine ratios and intensity into one table
• PCA analysis for each data type
• T-test for DE at each timepoint

Load libraries

Read in tables

Proteomic data preparation

• This code extract the information from proteinGroup file generated in MaxQuant and put them in a tidy format
  • intensity
    • Run Anders & Huber, 2010 method to get normalized intensity for each protein
  • ratio
  • normalized_ratio

QC.1 - Intensity and normalized intensity

Data preparation

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")
## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")

## Using Protein IDs, Gene names, Protein names, Fasta headers as id variables

## `summarise()` regrouping output by 'Protein IDs', 'Gene names', 'Protein names' (override with `.groups` argument)

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")

## `summarise()` regrouping output by 'nutrient', 'samplingTime', 'replicate' (override with `.groups` argument)

Box plot

Scatter plot

QC.2 - Ratio and normalized ratio

Data preparation

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")
## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")

## Using Protein IDs, Gene names, Protein names, Fasta headers as id variables

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers", "channel", "nutrient", "samplingTime", "replicate", "ratio")

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")
## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers")

## Using Protein IDs, Gene names, Protein names, Fasta headers as id variables

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers", "channel", "nutrient", "samplingTime", "replicate", "normed_ratio")

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers", "channel", "nutrient", "samplingTime", "replicate", "genotype")

Box plot

Scatter plot

Combine ratios and intensity into one table

## Joining, by = c("Protein IDs", "Gene names", "Protein names", "Fasta headers", "nutrient", "samplingTime", "replicate", "genotype")

## Using Protein IDs, Gene names, Protein names, Fasta headers, nutrient, samplingTime, replicate, genotype as id variables

## [1] 551664     10

##   Protein IDs Gene names                                 Protein names
## 1      Q9P305       IGO2                   mRNA stability protein IGO2
## 2      Q99385       VCX1              Vacuolar calcium ion transporter
## 3      Q99383       HRP1  Nuclear polyadenylated RNA-binding protein 4
## 4      Q99297       ODC2    Mitochondrial 2-oxodicarboxylate carrier 2
## 5      Q99258       RIB3 3,4-dihydroxy-2-butanone 4-phosphate synthase
## 6      Q99257      MEX67                      mRNA export factor MEX67
##                                                                                                                                             Fasta headers
## 1                   sp|Q9P305|IGO2_YEAST mRNA stability protein IGO2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=IGO2 PE=1 SV=3
## 2              sp|Q99385|VCX1_YEAST Vacuolar calcium ion transporter OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=VCX1 PE=1 SV=1
## 3  sp|Q99383|HRP1_YEAST Nuclear polyadenylated RNA-binding protein 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=HRP1 PE=1 SV=1
## 4    sp|Q99297|ODC2_YEAST Mitochondrial 2-oxodicarboxylate carrier 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=ODC2 PE=1 SV=1
## 5 sp|Q99258|RIB3_YEAST 3,4-dihydroxy-2-butanone 4-phosphate synthase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RIB3 PE=1 SV=1
## 6                    sp|Q99257|MEX67_YEAST mRNA export factor MEX67 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=MEX67 PE=1 SV=1
##   nutrient samplingTime replicate genotype      data     value
## 1        C          T00        R1 spike-in intensity  35919000
## 2        C          T00        R1 spike-in intensity  27087000
## 3        C          T00        R1 spike-in intensity 306210000
## 4        C          T00        R1 spike-in intensity  82491000
## 5        C          T00        R1 spike-in intensity 157850000
## 6        C          T00        R1 spike-in intensity  85041000

PCA analysis for each data type

T-test for DE at each timepoint

## Using Protein IDs, Gene names, Protein names, Fasta headers, nutrient, samplingTime, data as id variables
## Using Protein IDs, Gene names, Protein names, Fasta headers, nutrient, samplingTime, data as id variables

## Joining, by = c("Protein IDs", "Protein names", "Gene names", "Fasta headers", "nutrient", "samplingTime", "data")

## Using Protein IDs, Gene names, Protein names, Fasta headers, samplingTime, genotype, data as id variables

## Using Protein IDs, Gene names, Protein names, Fasta headers, samplingTime, genotype, data as id variables

## Joining, by = c("Protein IDs", "Protein names", "Gene names", "Fasta headers", "genotype", "samplingTime", "data")